How much time to allow for a flight from Athens connecting to Crete?

If you can get it on one ticket so that if you miss the 1.30, they will put you on the 5. Do it. If not, book the 5 and beg to get on the 1.30 if you are early.

You will not be able to have yours flights with one ticket with Sky Express as this airline does not have codeshare agreements with other airlines.

A single ticket USA-Crete would be only possible with Aegean/Olympic and/or another Star Alliance member (United, Air Canada, Lufthansa, etc).

So since you can't get USA-Chania flights with just one ticket, fly on Sky Express with no regrets

With Aegean you also have a 1:05 p.m. flight to Chania (25 minutes before the Sky Express). 125 minutes is a bit risky but in principle doable especially since you don't have checked baggage.

There is also the possibility of flying from ATH to Heraklion but this may not suit you.

I have done this transfer with no problem, even had time to grab a bite to eat in the food court in the departures area. It does depend on your incoming flight being on time. Just follow the transfer signage. When I have done it I have been traveling Air Canada/Olympic from Victoria to Chania so checked all the way through, just had to go through security before departure from Athens, whicj can be very crowded. Just make sure you go to the B gates which are domestic flights. I see Sky Express is not Star Alliance so you may have to check in on that flight in Athens.

2.5 hours is more than enough time.

2.5 hours is more than enough time.

...as long as the inbound flight is reasonably close to on time.

Does your cabin bag conform to Sky Express carry on rules? ( i.e., 8kg limit)