Which commuter flight do you recommend?

Either.
Just use the one more reasonably priced and/or more convenient for your needs.

These two airlines merged last year, so it doesn't matter which one you book.

Steve,

I've only travelled on Aegean and would absolutely recommend them. As both airlines are now owned by Aegean, I'm sure the service standards are much the same, so price and schedule convenience may be the points to consider.