In many of the locations you plan to visit, June will be crowded -- anytime after school is out will be crowded. June will generally be better than later in terms of the heat.

"I have been to the New York museums, except the Guggenheim"

Awesome! After YEARS of travel to NYC, during which I devote myself entirely to museums, I haven't managed to see more than a small fraction of its museums. But I have seen the Guggenheim, and visit it each time I go to NYC. Making time for it makes sense to me.

The National Gallery in DC is excellent. And you've already been advised to consider the wonderful Phillips Gallery.

Two days would not be enough in Boston for me. YMMV.

Enjoy!

Re: the Guggenheim: I should add that during times when the staff are setting up a special exhibit, parts of the museum -- which could include the ramp -- might be closed. So you might do well to learn what will be open when you plan to be there. I think the relatively small, but exquisite, core collection would likely be open even if they are setting up a special exhibit, but I could be wrong...