I like the analogy of staying on the property. If you read on this forum's Disney Resorts Board, everyone makes out like you'd be nuts to stay off property. Yet millions of people stay off property and have great Disney trips. Many of those people think you'd be nuts to stay on Disney property.
Staying in Jersey for a NYC trip is a great option for many people. I've done it, I've known tons of other people who have done it, and it works out nicely. It can save money, allow people to get a bigger hotel room or have their car with them. When my brother stayed at the Sheraton Suites (the hotel in Weehawken people were taking about) the boat ride into the city was their kid's second favorite part of the trip (nothing beats dinosaurs). And for a lot of people, they are a more comfortable staying in a hotel that is like hotels they've seen back home, rather than in Manhattan.
Whichever way you go, have a great trip!