Both NYC and Boston are water cities - their waterfronts are among their best assesses and in the past decade or so they have been enormously improved. At least for me, visiting the waterfronts (especially in summer) is the highlight of a visit to either of these cities yet I really don't see much mention of them on travel forums. I just read the last twenty or so posts about each city and hardly any mention of waterfront walks or ways to get out onto the water (with the exception of the SOL ferry).

NYC - Instead of standing on a line for 90 min or more AFTER you bought your Statue of Liberty tickets you could take a fabulous walk all around the tip of Manhattan. I love the route from North Cove around the Battery and up to South Street Seaport. Great views of the SOL, the Jersey skyline, the Brooklyn Bridge, etc. Cool, lively, free. There is much more waterfront that is now user friendly (http://www.nyc.gov/html/dcp/html/mwg/mwghome.shtml) but that's the best section.

To get out onto the water and see the city from it's best perspective you can take one of many cruises but there are two free ways - the Staten Island Ferry, and on weekends NYC Taxi runs a free ferry from Pier 11 (just south of South Street Seaport) to Ikea in Brooklyn. It's 20 min each way (runs every 20 min). You can just turn around and come back or go into Ikea - even if you don't want to shop they have a nice cafeteria for lunch. During the week that ride is $5. And for $25 you can do the Water Taxi hop on hop off which goes from west 44th up to east 44th (although I don't think you can get off up there, but there are several other stops).

Boston - after the seemingly endless 'big dig' Boston water front is now gorgeous. The most visited section is Long Wharf (right across from Quincy Market) which is where the Aquarium is, but also a lovely park and lots of benches and place to sit and watch the boats (or the planes landing and taking off from Logan across the harbor). You can take a ferry from there over to Charlestown which is where the USS Constitution is parked. Great views of the harbor. Take the ferry back or walk back (about a half hour) across the bridge and along more of the waterfront. The cost - one metro ticket. Boston also has the Esplanade all along the Charles River - which, given that it is a river is in fact more waterfront.