We flew with Continental from Heathrow to Newark a couple of years ago, and actually went transatlantic on a Virgin plane, with the internal flight down to Orlando International on a Continental plane-it's called a codeshare apparently.
When we arrived in Newark, had we been sitting on the left hand side of the plane, we'd have had a brilliant view of the Statue of Liberty in the early evening sunshine.
Try and book your flight as soon as it's released by the airline-it's different for different airlines, but roughly 11 months before you actually fly.
As for New York hotels, there are loads to choose from-where and which depends on your budget. We stayed in a Best Western very close to the Empire State for 3 nights, which we found good, and very central. Needless to say, 3 nights wasn't really enough, but we managed to pack in an enormous amount of things, including all the major sights and meeting up with some cousins too. It also gives us an excuse to go back sometime!
It was a great stopover before all the parks, etc in Orlando.
We booked everything ourselves, and have done so on all our holidays since. We wouldn't go on a package holiday again, as doing it yourself gives you more flexibility, it is definitely cheaper, and all the planning is part of the fun!