The ferry ride really isn't that long and it's very scenic. The only problem is the wait for the ferry itself (unless you're walking on).
There are plenty of outdoor activities around San Juan Island itself and especially Roche Harbor. Go whalewatching, kayaking, fishing, hiking, etc. I'd also recommend hopping over to Orcas Island if possible--it's also very beautiful.
http://www.rocheharbor.com/