If it were me (and I know it is not!). I would choose Titicaca. We spent a few months in South America and decided not to visit the Amazon, mainly because we had been to many rainforests around the world (Borneo, SE Asia etc.) and there was lots of other stuff to see in Peru.

We had fully intended to cross the lake and make our way to La Paz but there was some trouble in the country at the time and they closed all the borders so we made our way to Arequipa instead.

I am pretty sure you cannot get a direct flight to Cusco and will have to route through Lima as you have already booked your IT hike you should fly on to Cusco asap in order to begin acclimatisation asap befor the hike. NB Age/sex is no indicator of how you might or might not be affected. See:

http://www.nhs.uk/conditions/Altitude-sickness/Pages/Introduction.aspx for further info.

The Sacred Valley apart from MP is always worth exploring as you are in the area,

See also www.sexplorers.org may be worth joining for the club houses, discounts etc.

Some photos and more info on our time in the area on our blog Entries #55 on cover Peru http://blog.travelpod.com/travel-blog/candcthai/1/tpod.html

Do let us know what you decide.

I see you're from Edmonton. I just wanted to say have a good time (from Ottawa). Our guide on the IT kept saying come back in June. We started on December 31 and had very good weather. But every time someone would rave about the weather he would say come back in June.

So I think you have picked a good month.

Tough choice, we decided on Puno/Titicaca but we live in Equatorial Africa, so it was an easy call! All I can say that either would be great

Lake Titicaca definitely. And do a homestay on one of the islands. A highlight of my 5 months in South America for sure.

Thanks everyone for your replies. We were leaning towards Lake Titicaca any ways, and I think this helps make our choice a little easier.

Lake Titicaca & the Amazon are two of the main attractions of my country. Both destinations are highly recommended. If you want to enjoy a unique wildlife, the Amazon is the best choice. It's important to mention that in Peru you have the Amazon (north) and the Rainforest (south).
Lake Titicaca is amazing and a day in one of the islands is highly recommended. You also have to know that an extension trip to Lake Titcaca is cheaper than to the Rainforest or Amazon.
If you decide to visit the Lake, you could visit one day the Peruvian side (Uros, the floating islands are a must there) and the other day take a full day to the Bolivian side; the only problem is that Canadians need visa for Bolivia and they are more than US$140.
Good luck!

I stayed in Cusco for a month a few years ago. I was lucky enough to do trips to Machu Picchu, the Amazon, and Lake Titicaca. If I were going again, I would definitely choose the Amazon over Lake Titicaca.

Although the Lake is beautiful, it feels a little too touristy and there are a million things to do and see in the Amazon.

Good luck!

Thank you all for your replies again. I think we're more inclined towards the Amazon trip now and we're wondering if anyone has any recommendations for an itinerary. Would it be possible to arrange this part of our trip with a travel agent/tour group in Cuzco when we get there, or do you think we need to pre-book?

I haven't been to Lake Titicaca, but I love the Peruvian Amazon so much that I've been there three times. I always go through www.explorama.com (The ExplorNapo camp is my favorite.)

There are lots of operators in Cusco where I am sure you will be able to book a trip on arrival. The problem is there is no real way of knowing how good or bad each one is. I would suggest doing some research and book before you arrive. Do take care if asked to wire money beforehand. Paying by credit card will provide financial protection. Better still pay on arrival in town.

The following websites are trustworthy and a good place to start:
http://www.saexplorers.org/destinations/cusco
http://www.andeantravelweb.com/peru/index.html

We found our guide for the Lares to Ollantaymbo trek at SA Explorers and it was one of the best experiences of our 5 months in South America.

If you're looking for a real adventure in the Amazon, I'd recommend you Tahuayo Lodge. They are located like 4 hours away from the city and offer tailor made programs. They have activities as night walks, piranha fishing, canopy, visit to shamans, etc. Muyuna Lodge is also very nice. Always look for lodges away from the city otherwise your adventure in the Amazon won't be so real.