Ticketed cruise passengers who are using the Black Falcon pier could park for $14 per day last year:

http://www.massport.com/ports/cruis_parki.html

But as wyatt advised, Boston parking is never "nominal".

I would rethink the itinerary.
Spend Friday and Sat. in or near Boston. Stay at a place near a MBTA stop. Cruise Sun to Sun. Park at the cruise terminal.
Spend Sun - Tues on Cape Cod. Provincetown is only 2.5 hours from Boston. I would look at a motel in Wellfleet. The Even Tide is very family orientated. I like the Outer Reach Resort in Truro.
Drive back to Toronto with a stop in the mountains.

4trip,
Just so you know, the ferry to P-town last I heard does not allow cars. Not sure if you were planning on driving to Rockport from there.

At any rate, P-town is extremely walk friendly. Lots to do - biking, beaching, great sunsets, ex. people watching,kayak rentals, whale watching and fishing trips and a beach dune tour (Arty's)

Although not luxurious, The Cape Inn in P-town should be fairly inexpensive - don't know if they'll book one night only, though, most won't.
It's across from a beach and on the trolley run to other beaches, the center of P-town and other towns on the cape, as well as being within walking distance of the center of P-town.
They have a restaurant.

http://www.capeinn.com/rates.shtml

raineday,
Thanks I think your plan makes a lot of sense. I have been banging my head against the wall looking for suitable accomodation in Boston ,when in the end I think we would be much happier on the Cape anyway.
Thanks for the hotel suggestions for the cape everyone, I will look into them and probably book something soon. I haven't done much research but I am assuming that Provincetown is still our best location given that the national seashore is there, and there seems to be a lot of activities. Not that it matters too much ,but what temperature can we expect the water to be? We swam off Cape Breton so I am assuming it will be at least a little warmer.
I think we will bite the bullet and book something near the cruise terminal on the Sat. night before the cruise so that we can maximize our little time in Boston . We were looking at the Park Plaza which is around $200.00. Does anyone know if this is a good choice?
Thanks so much everyone for your help, trip planning is fun but difficult.

Check out Orleans and Wellfleet also for lodging options - also close to the National Seashore.

For the hotel near the cruise, check out the Westin Waterfront- usually available on weekends for a very reasonable price as it is not as convenient to tourist areas of Boston as many other hotels. Also the Seaport Hotel. Both are very nice hotels.

Well, the Park Plaza is not near the cruise terminal, but otherwise it's a great choice and that's a very good price. On a Sunday morning you'll have no trouble with traffic.

The National Seashore is huge and is not just is Provincetown. Check their web page for maps. And we just want to make sure that you know that Provincetown is a renowned gay-friendly arts colony.

Water temps on Cape Cod will be similar to, or cooler than, Cape Breton. The bay side temps will be warmer than the ocean side.

Anonymous,
Not to worry, they are pretty upfront about it on the website. I have a lot of gay colleagues, and actually think it will be a good cultural experience for my children.
Cybor and raineday
I booked the Cape Inn as suggested. They had a special early booking deal and booking for only 2 nights was not a problem, as it was with some other places. It also has really good reviews on trip advisor.
We ended up booking the Boston Hilton Financial District for $216 plus $38 parking (yikes). The deal at the plaza fell through as it was a multi night deal.
I will now have to look into what is not to miss in Boston and Provincetown.
I am leaning toward the Freedom trail and Faneuiel Hall. Anything else we shouldn't miss? Any interesting eateries that kids and adults would enjoy. (again budget minded).
In Provincetown I am sure it will be biking , hiking , hopefully some seafood and maybe a little shopping if i wear them down enough. Any recommendations for stops on the drive up to Provincetown (or maybe the drive home)?
Thanks for your help everyone.

Is there some reason that your husband can't take the boys for an hour or two so you can shop either in Boston or P'town? I don't even like to shop but I'm starting to feel sorry for you!

I'm sure it will happen. I am not actually a huge shopper myself but a little is nice, so i'm sure I can lose them for awhile. It is the family joke though, so I have to complain about it.

Both P'town and downtown Boston provide a nice human-scale mix of sightseeing, small museums, options for touristy hiking around just gawking, and shopping opportunities.

Everybody will enjoy the "Geoclassics" store at Faneuil Hall Marketplace (eastern end of the northern building): Fossils, crystals, AND jewelry! If they get bored, send them across the way for ice creams.

Yes feeding them is always good. They will get one for me too , and then eat it. Sounds like a great shop, they also enjoy any kind of back country outfitter stores. I can usually send them into those and go off on my own.

They might want to check out Hilton's Tent City, which is in between Quincy Marketplace and North Station. An old Boston institution. The staff are very well-informed and down-to-earth; no foofy REI climbing rocks for them!

http://www.hiltonstentcity.com/store.htm

Welll, you could shop while they ride bicycles in Boston - they might enjoy that - there are some great bike tours available that would occupy them for 1/2 day or more if they like - I think most of them start around 8:30 and are about 4 hours long....you could all still meet up for lunch and the rest of the day !

Google Esplanade Concerts and see if something is going on while you are here - the whole family would enjoy that - walking thru Boston Common and the Public Garden down Charles Street and over to the Charles River for a great evening concert -

also, see if they are still doing the night time family movies outside on the wharf behind the Rose Wharf hotel -

here is a sight that might offer some ideas:

http://preview.tinyurl.com/3bw9ox

There is also a short historical presentation and a great view from the Skywalk Observatory at the Prudential Ctr the boys might enjoy ( and you could shop in the Pru Shops/Copley Place.....) if you don't care about views....

The tour of Fenway Park is a great idea - check out the day/time on their website b/c it varies if htey are playing in town or not - but we always take visitors on that (or my husband does while I shop with their wives

I guess it is my own fault I don't get to shop. The bike tour is very intriguing, and no way would I pass that up. We are a big cycling family.
I imagine it would be a good way to cover alot of ground, I checked briefly on a website and it said 10 to 12 miles. I need to look into it further though because I think I would like to feel free to stop where we wished. There was a freedom trail one and a Boston Neighbourhood one. I am assuming that the Freedom Trail would be the one to go with.
I like the other ideas too, and will investigate further.
There are too many things to do, we could stay for a month.
Continued Thanks for everyone's help. Much appreciated.

4Tripping:
many of the bicycle tours also do private tours for you specific group - and most of them make stops - so perhaps you can get exactly what you might want !

the Emerald Necklace would be a beautiful one too !

My husband now just wants to rent bicycles and go around on our own. Would this be a good way to see the city, or would we be better on foot?
A private tour is not out of the question , but we don't think we would enjoy a group tour. We would have to bring locks for stops obviously.

Just to clarify my previous question, can you ride on the trails? Are there cycling lanes? Do the paths get so congested that cycling is unrealistic?
Thanks again

If your family are all good cyclists, then yes, you can rent and ride on your own - having some city cycling experience of course, is always helpful - but yes, there re those who do - my son bikes all around the city, from the South End to Cambridge and Harvard Square - the Emerald Necklace, etc - my husband and I are not as adventurous as my son in the heavier traffic areas, but we enjoy

there are some excellent bike guides, I would suggest you get them beforehand so your husband can plot your course and familiarize yourself with the area, where you might want to go, etc.
The link below lists all the bike paths, miles, locations, etc

It also has links to a great bike map, guides etc of the city - including the car free Boston guide -

www.massbike.org/resources/

And here is a tiny url link to great link for cycling in Cambridge -

http://preview.tinyurl.com/36jgdm

And you are LUCKY ! You are here on a Sunday - might be a good day to cycle - since they close section of Memorial Drive for cyclists, skaters, etc - which is great fun - (more my idea of cycling in the city) - you can access that through either the Cambridge link -
or just google - Memorial Drive closed for bikes, I'm sure it will come up with a map, etc to help your husband plan

Biking is a great way to see the city and feel like a resident and not a tourist ! You can also stop whenever you want - for breaks, lunch, etc -

and there is nothing
Also, I would suggest walking a portion of the Freedom Trail that is so close together it would be more of a hassle (to me anyway) to have my bike -
the Boston Public Garden/Boston Common/ Granary Burial Ground, the sections that are extremely close toegether and in high traffic areas both on the streets and the sidewalks -

you can , I think, probably figure this out by using the Freedom Trail guide along with the biking guides -

thefreedomtrail.org

You will need a lock, but I am sure they will provide with the rental - and some rentals will drop off/pick up also

so.......I see your shopping hours dwindling