We have hotels booked, Charles in Cambridge and Francis Melbone in Newport.
Any recommendations on sites, restaurants?
What about Cape Cod? Any ideas for a day trip?

We've been to newport a great deal, we used to get summer rentals there with our friends when we were younger 20's....1994 for me.
great restaurant for casual eating is the Red Parrot. the inn you are at is right on thames st., the main road of the harbor/village area. plan on walking to dinner,etc, b/c parking in newport is SCARCE. however, it's best to stay in town, and drive to the beach.
btw, we have a gift cert to the same inn tha you are staying atthat we are planning on using in october, we've never been there, but have been told to request a room in the back, b/c the front rooms get noisy b/c of street traffic. it may be too late for you to change your room, but i would think this would be a big concern in summer. what if anything have you heard about it?
obviously go see some mansions, beechwood is my favorite b/c they have costumed staff who plays characters from the past.
as far as the beach scene, it's not a great beach as far as east coast beaches go, but the draw in newport is the nightlife, and the mansions. if you do go to the beach, i believe the one you should try is First Beach, they have a fun beachside bar that has bands, etc. if you want quiet, then go to second beach.

Cape Cod is lovely but unless you really like sand and dunes, I prefer the Sandwich area and the drive along Rt 6A. The Daniel Webster Inn was recommended for dining. Along Rt 6A there are plenty of sideroads leading to wonderful beaches, bike trails in shaded areas, and fun shops. We stopped at the Dunbar Tea Room across from the Thornton Burgess Museum in Sandwich for late afternoon refreshments. The lunch menu looked great. It was a cold rainy Easter weekend so a hot cup of tea in a cozy place was just right. But you can also have a nice drive around RI, Tiverton and Greenwich are fun. Don't forget to have a coffee cabinet (milk shake).

Newport has many so many things to see and do, you really need to spell out your interests. For example, if you are nautically inclined you could spend a day or two just renting a sailboat/or taking a sail tour, visiting the international yacht restauration school, Herreshof museum in Bristol, etc. Diving? Theres the wreck of a WWII u-boat for experienced divers, other sites for less expereienced. History? Haffenreffer museum(sp?) in Bristol will start you off with early native american culture, a walking tour on historic hill will bring you up to colonial times, mansions for the guilded age. Scenic drive? Ocean drive out past Fort Adams (stop for a visit) past Castle Hill, ending up on Bellevue Ave past the mansions. Think about taking a helicopter tour of Aquidneck Island. Day trip? Block Island. Of course, If you like night life, Newport is the place (OK, it's not the Village or South Beach but pretty good for a New England equiv.) I agree with the above about the beaches, but if you just want to lay in the sand and get a tan, hey, good enough.

In Boston, I suggest eating in the North End to get some wonderful Italian food. You almost can't go wrong in your choice of a restaurant. I had lunch in Artu recently and it was delicious. Marcaccio(?) is also supposed to be wonderful.

For a nice dinner in Cambridge, try 'Upstairs at the Pudding'. Lovely place - try to sit outside on the roof deck if the weather is right. Pleasant walk from the Charles. As the name says, it is upstairs from the Hasty Pudding Theater - some history there.

For Boston - depends on what you like. I live in Boston, and would be happy to provide you with a list of places to try if you give me more specifics - French, Italian, etc...