I am US citizen going on a Canadian cruise. I want to disembark on Boston which is two days early. Will the port Authority allow this? Will customs be available?

On the days when the cruise ship are in port the Custom department are there too, the cruise ship leave out on Fridays and Saturdays

If the cruise starts in the US other than Boston, you will not be able to disembark in Boston. If it starts in Canada you might. Cruise line must approve and arrange it.

Check with your cruise line to find out if you do that. I doubt customs will be available as is not a disembark stop.