We've gone both ways. Depending on the conditions, if it's a delivery I'd choose offshore. Then you don't have to deal with land masses and you get to sail a lot more.
If it's a cruise, I would definitely choose the Bay route for all the wonderful anchorages. As posted earlier, just keep in mind that you must
follow the tides up the Delaware, you cannot
sail the Canal, and you may
find some wind in the Chesapeake depending on the time of year. We just posted a few articles about the Chesapeake at www.coastalboating.net
and are in process of writing one about the different routes (offshore vs inland).
Either way you'll get a lot of BIG ship traffic - offshore you'll be crossing shipping lanes, inshore you'll be sharing them. Hail them on channel 13 if you can't determine their intentions. Takes alot of the stress of crossing and meeting situations out of the equation.
As to the stops, we've only stopped in Cape May, Sandy Hook, Block Island, and Montauk, but you can surely spot the lights of AC from 30 miles off. Like a Christmas tree and a good stop in bad weather (I've checked it out by land). Both Cape May and Sandy Hook are great staging areas for hops.
We've also transited the East River and it's not a big deal if you time your transit with the tides. Hell Gate can be quite fun - a real sleigh ride. Best part is going faster than the cars sitting on the East River Drive. We have an article about that posted on our website as well.
Either way, it's a great trip. Enjoy!