An economical way to see Boston by water is to take the MBTA harbor ferry from the Aquarium (Long Wharf) to the Charlestown Navy Yard and back. The Ferry runs every 15 minutes, so there is little wait. It costs $1.50 each way, and gives you a great view of the city.
How can you beat $3 for a round trip Boston harbor cruise.
Many people prefer water-shuttles & ferries to get to & from Logan Airport or to & from the North & South Shores. See http://tdc-www.harvard.edu/massbike/info/ferries.htm for a list & additional links for water transportation.
We took a ferry from Charlestown (the end of the Freedom Trail), back to downtown Boston. It cost $1.25 one way which wasn't bad at all. The ride itself was less than 10 minutes.
Photo: You can't tell, but it was very windy on the ferry! You can sort of see Boston's downtown skyline in the background.
For a city struck out into the Atlantic on a peninsular of land, it's not surprising to find Boston has ferry services to shuttle people from one place to another. The ferry services form part of the MBTA system that includes buses and underground trains. They operate across Boston harbour and offer great views of the city for just the price of a ticket. They are even free if you bought a travel pass for that day.
A good way to get to the USS Constitution in Charlestown is to take the water shuttle. Operated by the 'T' it leaves from Long Wharf every half hour. It's a short trip, taking less than 10 minutes to cross Boston Harbor. But it is a very scenic ride, with good views of the Boston Skyline and The Old North Church in the North End. Be aware though that the shuttle docks on a different wharf from the USS Constitution, and it's about a 10 minute walk through the Historic Charlestown Navy Yard to get to Old Ironsides.
Long Wharf is located at the Aquarium 'T' Station on the Blue Line. The shuttle is a bit hard to find amongst all the tour boats.
When flying into Boston, take the appropriate shuttle to the "Water Docks" . Normally there are boats waiting but sometimes they are not there and if that happens to panic. There is a small box that has a button, just push it! They are never longer than Five minutes and its a great ride! If this is your first time to this Tea Town, try the Water Taxi, Its a view to remember! Be sure to check the operating times before you go!
If you arrive at Logan airport, the nicest way to go to downtown Boston is to take the waterbus: at $10, it's more expensive than a subway but much cheaper than the taxi and so much more agreeable!