all excellent recommendations/comments.
I found Nicaragua harder to travel in than some of the other CA countries because a lack of tourist infrastructure and also general lack of numbers of people. I went to Tierra tour for about a week looking to hook up with others on specific tours and had to wait a lot. (this was October).
You might find it useful to hook up with others on an overall tour, i'm not sure - see
http://www.explore-central-america.com/travellers_wanted.html


Thanks to everyone for all the informative posts. A bit confused about the differing opinions on the weather.
I have a follow up question about Leon: Will it be as lively in the middle of June if the Universities are done for the semester? My Spanish isn't the greatest, but I was looking forward to the City being filled with University students. Any advice if I should head up there for the begining of the trip or the end? Unless I head up to the mountians, I'll probably be around Granada and Ometepe for the rest of the trip.
Hopefully everything works out as far as joining up with some groups for the daytrips. Any advice on tour operators? I see Tierra Tours name mentioned a lot on the boards, but someone said that they weren't that great for the kayaking trip.
Thanks again for all the great ideas!
Leon is full of students no matter which time of year you go.
If you take public transport chances are you will meet people on the bus/boat who are heading where you are and want to do the same tours. Tierre is great. When in Granada ask for David. He helped us organize our boat tour of the isletas than the next day offered to drive us to San Jorge. It was amazing. He took some 'off the beaten path' roads and taught us a lot about the country side and the people.
How much time do you have?
I had 2 months and did Ometepe twice, Granada, Apoyo twice, Masya, SJDS (blah), Playa Madera, Rio San Juan (awesome) San Juan Del Norte (hottest place I found in Nica) Bluefields twice but only as a stopover, Big and Little Corn (Little Corn is better) El Rama, Estili, Miraflor (interesting), Somoto and the Canyon of the same name (coldest place I found and the Canyon is a MUST).
I recommend to everyone not to spend your last night in Managua. I had one night there when I was seeing my friend off at the airport and that was enough for me. Because Managua is so close to many great places there is really no need to spend much time there. I generally love big crowded sensory overload type cities but Managua is not one of them.
I flew in and went to Granada (30 mins) If you arrange airport pickup make sure your driver is aware that it is included in the price and don't give him/her any money unless as a tip.
My flight Managua at 1am and I didn't leave Apoyo until 10pm. It's about 45mins and if you stay at Craters Ann will call her guy to drive you. I paid $17 but it may have gone up. It was the perfect way to end my time in Nica.
I'm also going to rave about vianica.com It was an amazing tool for planning my trip.
Have fun