We would like to Rent-A-Car for a day trip to go from Boston to Martha's Vineyard area. Any recommendations on the best place/reasonable place to rent a car for this trip? Is it better to rent a car slightly outside of the city center or is the price about the same?
I would take a Peter Pan bus from South Station which goes right to the ferry and then rent a car on Island. It would be much less expensive that way and you will avoid having to drive to the ferry and then park near the ferry and take a bus to the ferry ( That is how the parking works) or pay for the car to come over on the ferry.
You could also take the Peter Pan bus from either Logan Airport or South Station to Woods Hole. It runs several times daily. The bus drops off right at the Steamship Authority in Woods Hole. Otherwise, if renting a car and driving, $12 parking/day at the Steamship Authority Palmer lot and a short bus ride (provided by S.A.) to Woods Hole.
Going from Boston to Martha's Vineyard for a day trip is not something I would recommend. Especially in the summer. Ferry reservations are difficult. If you are set on that then I reccomend taking the Pied Piper and land right in Edgartown... A very walkable town in MV and you won't have to take a car. Or, as an alternative, take the ferry from Boston harbor right into Provincetown on the Cape. Can be done in a day.
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In general, car rentals will be cheaper off airport because the taxes are less. The major brands have offices spread throughout Boston, so I'd just do a kayak search and pick the best overall price as they are all easy to walk to or take the T.
The drive to Wood's Hole isn't that long, so if you have the time, I recommend meandering and taking 3A through all the coastal New England towns rather than Rte 3 (which is more of a freeway). The drive will be nice, though not as memorable imho as if you drive north of Boston toward Maine. Note: If you want to drive only to go to Plymouth Rock, set your expectations very very low. However, the town itself is actually quite nice.
And you haven't asked, but I assume you may be thinking of taking the car to MV... depending on how long you are staying will really be the answer. If just a couple days, then it's not worth the price. The island has good public transportation and cab services. If the stay is longer, however, then it might be a consideration.
Note: This is all assuming you're going there soon, in the Fall or Winter. If this is a summer-time journey, then driving will be way more hassle than it's worth, both to Wood's Hole and especially on the island.
I would recommend renting the car from Boston Logan International Airport. The competition from all the brands being represented there breeds the best prices. I would still make a reservation first, using a travel discount site like Expedia or Travelocity, as these reservations rarely make you pay up front. The other benefit to renting from the airport is all the public transportation options to get there.