I'm also currently planning a trip to Greece (mostly Crete) next September, so I've been going down this rathole, too, for months. Short version: There are (of course) no flights to Crete from anywhere in North America, so you will need to connect somewhere else in Europe. Many people choose to connect in Athens, and that's an obvious and often logical choice. But there are oodles of other places you could connect if you find that better. I haven't counted, but there are probably over a hundred options - name any large city in Europe, and there's probably a flight to/from Crete from there. One caution: Many (in fact most) of those flights are highly "seasonal" - only flying during peak tourist season (in med-September, when you are going, it's right on the trailing edge of the season - be careful and check availability for your proposed dates carefully - do not assume a return flight will still be going in late September, many have reduced schedules or stop flying entirely by mid/late September). Still, you have lots and lots of options, including some surprising ones (I'm flying to Crete from Seattle via Helsinki Finland, probably not a route that most people would think of - but I got a great deal on a flight, and it works nicely for me).
Here are snapshots of where you can fly to/from for both Chania and Heraklion. Look at all your choices!
Flights To Crete
There are two major airports on Crete that get virtually all the flights: Chania (CHQ) and Heraklion (HER). Most folks say they like Chania a lot more than Heraklion, but both get a lot of flights (Heraklion actually looks to get a few more than Chania). There's also a third airport, Sitia (JSH) at the eastern end, but it's small and only has a few domestic flights from elsewhere in Greece.
You have LOTS of options. My approach is to work on the long transatlantic flight first (because I'm more picky about that, since it's way longer - and overnight), find something I like for that, and worry about the relatively shorter connecting flight in Europe second. Others have their own strategies.
About stopping to spend a couple days in Venice or elsewhere before proceeding...I'll just add: Crete is big, really big. Many savvy Greece experts suggest you need a LOT of time to see Crete - more than almost everyone expects. I'm gonna have 11-12 days there and that's too short to get all around the place. If you hope to "see it all" (or even see half of it) you might reconsider stooping en route to spend a few days relaxing, and save those days for Crete itself, since you will have to make hard choices and trade-offs anyway. Just something to think about.
Hope some of that helps.