Do you mean Friday Harbor (on San Juan Island) AND Orcas Island? You could end up spending quite a lot of time in line waiting for ferries. The main ferries take reservations, but the inter-island ferry does not. Most of the locals on the TripAdvisor forum advise sticking to either Orcas or San Juan Island for a short trip. Most of the whale-watching tours depart from Friday Harbor.
You will have to be careful with dates, as by mid-October some of the whale-watching tours and kayaking tours will have ceased. I saw a last date of October 17 for one whale-watching boat, but I did not check others. And for kayaking, I saw end dates of Oct. 7 and Oct. 13. One place on Orcas did not offer any guided kayaking in October at all. And the San Juan’s are not a place where you can just rent a kayak and go without a guide—-the tides, currents, and changing conditions make that unsafe, unless you are deep in protected harbor.
Early October can be really nice up here, but in my experience (from 30+ years of living here, and spending lots of time outdoors hiking, biking, and kayaking) the weather generally “turns” in sometime mid-October and becomes cold, cloudy, and/or rainy. So the earlier in October you can come, the better.