My concern would be the on-time performance of the AA flight getting into KOA, check the stats of the flight and plan accordingly. If you didn't check any bags on your AA flight and didn't have to wait for them, I would think the 3:25 pm flight would be the safest, and if you get there earlier, you might be able to get on the earlier flight if they have room. I did the walk between the commuter terminal and the main terminal, it really wasn't that bad, maybe a 10-15 minute walk at most at a relaxed pace. The commuter terminal is essentially a bunch of office trailers joined together, tour flights are based out of there as well. You'll be passing by the cargo building to get to it, so you'll be walking on the side of the service road once you leave the airport terminal part of the airport. The good thing with Mokulele is that there are NO security lines to go through whatsoever!! You check in at their counter, then wait by the gate of the airport fence for the pilot to summon passengers for the particular flight.
Mokulele's carryon policies are rather strict, but understandable because the small planes really don't have any space in the cabin for anything more than a briefcase or purse under the seat in front of you. It's been over a year, but didn't think the checked bag fee was much for our two carryons. Check their website, they have it published somewhere.
I kinda find Mokulele to be a charming airline to fly with, you fly low in altitude, and every seat is a window seat and the views are wonderful. The flight we took was low enough to see the whales in the ocean! I really didn't mind that it took a bit longer for the flight vs Hawaiian.
Otherwise, Hawaiian would be an easier transfer, especially if your AA flight gets into the same part of the terminal. KOA is a *small* airport, the lounge is outdoors, you walk on the tarmac to get on/off the planes!! Depending on the time of day, the security lines can be rather long, so be wary of that.