Rainier is definitely too far for a day trip. As for visiting the San Juans and kayaking, it's 90 minutes from Glacier to the Anacortes ferry, and you'll need to be in line about 90 minutes early if you want to take your car, then it's another 1+ to the islands. So that's pretty far for a day trip. An exception would be if you walked on, rather than bringing your car (you can park it at the ferry dock), and went to Friday Harbor on San Juan Island. You could look and see if there are half day kayak trips out of Friday Harbor that would work with your schedule and the ferry schedule.
Another option is to go to Lummi Island, close to Bellingham, and sea kayak there--I know there is at least one outfitter. It's a very short ferry crossing. It's on the edge of the San Juans, so it's not quite as spectacular as being in the middle of the islands, but its still quite pretty.
Its true there is ample (and world class) day hiking near Baker/Glacier, but it's also true that Rainier and kayaking the San Juans are incredible things to see/do. Can you tack one of those on at the beginning or end of your trip? Rainier is fairly convenient to Seatac, which I assume you're flying in and out of.