Kennebunkport, Cape Cod or Martha's Vineyard
 

My family which includes 4 teenagers and a husband will be in Boston in mid June. We would like to spend a couple of nights on the coast. We hear great things about all. We are looking for whale watching tours and activities along that line. Any recommendation on these towns? And where to stay? We are thinking on the water? But are happy to walk? Always hard to find rooms for 6?

The latter two are not towns. Cape Cod is a pretty large peninsula, upper and lower, with many towns of varying character.
Martha's Vineyard is an island, also with many towns that are not at all alike.
All have activities. All may have accomodations on or close to the water, at a price. A house rental may be a good alternative for 6 and at that relatively early time (before schools get out), you may be able to get less than a full week's rental.
I'd suggest you watch a lot of YouTube videos shot in those areas to get a better idea of what the possibilities actually look like.

Cape Cod would offer the best variety of things to do on and off the water. From Hyannis on Cape Cod you can easily take a boat ride to Martha's Vineyard and spend a few hours or the day. Martha's Vineyard is pretty, but is smaller and more a place to relax and rest.

I have not been to Kennebunkport, so I'll let someone else comment.

We stayed for many years in West Harwich, Cape Cod. We had a house there and the familial overflow stayed down the stree at the Commodore Inn/Motel. They have a pool and are like a minute from the beach. We sold the house and now stay at the motel.

Stayed in Falmouth myself on the Cape. You can take a ferry to Martha's Vineyard for the day if you want to see both.

Kennebunkport is a very nice little town, however mid June can still be a little cool, especially on the Maine coast. As someone else mentioned, Cape Cod is quite large, with hundreds of miles of beach, and dozens of towns. Some areas are quite developed with strip malls and mini golf, other areas are quiet and relaxing. If you are considering going in the water, the southern coast of the Cape and Martha's Vinyard would be your best bet, as water temps are considerably warmer. Even these beaches will still have cool water this early in the year however.