If your primary objective is to see the whales you should spend time at Friday Harbor (south) or Roche (north). Roche is busy but I'd consider it a must for a trip like this. You can either tie up to the dock or anchor out in the harbor. You can go up the inside from Friday and then around the island from Roche. Whales are usually somewhere along the SW side of San Juan Island so you will probably find them before getting back to Cattle Pass to go back to Friday Harbor. Make sure you have GPS and/or charts, there is often fog in the morning this time of year. I was just in that area on Sunday fishing off of Eagle Point. There's a bunch of humpies there which are easy and fun to catch, and not bad, but not the best eating. I like them smoked or BBQ'd. It helps to bleed them and put on ice right away. Troll flashers and squid or spoons, 30-70ft deep or cast pink jigs. I did manage to catch one king about 15lbs to go with 3 humpies for my limit. For more fishing tips look up John's Sporting Goods newsletter.
Good luck, it is beautiful in the San Juans right now!