Any suggestions for Boston that are close to historic sites and museums?
Also any idea for hotels on Oahu near Pearl Harbor?

There aren't any hotels "at" Pearl Harbor. Look in Waikiki for hotels. It'll be about a 20 or 30-minute drive to Pearl Harbor.

Are you flying into Logan? How long are you expecting to stay in the Boston area? The last time we stayed in the Boston area (long ago) we stayed in a hotel in Braintree and rode the "T" red line into the city.
There is a free shuttle from the terminals at Logan to the Silver line of the light rail. If you are flying in there is no need to rent a car. We enjoyed the Science museum which has 2 Van de Graff generators made by Mr. Van de Graff himself. For a demonstration a man stood inside a steel cage and had a lightning bolt come from the head of the generator to hit the cage.
Let us know what you find for Oahu hotels/motels.

Godfrey Hotel, Kimpton Nine Zero, or the Parker House. Next to Boston Common, T stations for the Green, Red or Blue lines are all within a few blocks, and you're walking distance to everything including the harbor, Fanueil Hall, Public Market, The Aquarium, The State House.

Harbor Arms is a hotel near Pearl Harbor, it's a weekly-apartment style hotel that mostly caters to military families. Its a 20 min drive into Waikiki or about an hour bus trip.

For Oahu, most people stay and I believe you would be happier in Waikiki. Exponentially more choices there.

If you tell us what month, and a general nightly price range we can make some specific suggestions. Also any amenities - do you want beach-front, will you have a car and need parking, do you want a view (if yes does it have to be the ocean or can it be DiamondHead, mountains, city view) and so forth???