Due to its closer proximity to Haro Strait, San Juan Island [1] is better suited for heading out on an orca adventure than Orcas Island [2]. However, if you won't be on San Juan, you can still find a couple of quality companies heading out from Orcas.
One of the most comfortable rides is aboard the 50-foot cruising yacht run by Orcas Island Eclipse Charters (360/376-4663 or 800/376-6566, www.orcasislandwhales.com [3]) in Orcas Landing. Eclipse guides Dan and Denise Wilks are contributors to the Center for Whale Research and they even played bit roles in the movie Free Willy II.
Another excellent option is Deer Harbor Charters (360/376-5989 or 800/544-5758, www.deerharborcharters.com [4]) in Deer Harbor, the longest-running whale-watching business on the island. The smaller vessels used by this company run on biodiesel to make as low an environmental impact as possible on the whales.
Links:
[1] http://www.moon.com/destinations/washington/san-juan-islands/san-juan-island
[2] http://www.moon.com/destinations/washington/san-juan-islands/orcas-island
[3] http://www.orcasislandwhales.com
[4] http://www.deerharborcharters.com