Hello! We will be traveling to Crete for 5 nights in mid-October of this year for our honeymoon. I understand the weather starts to shift about this time and there could be rain - we are fine with that although we would still like to maximize warmth/dryness. We are flying into Heraklion and flying out of Chania and have a one way rental car already booked for our dates. Where would you recommend we go? We want to stay in Chania at least 2 nights but have read that the south/east side of the island can be warmer and drier than Chania area. Should we just stay in Chania the whole time and use it as our base for hiking, beaching, exploring or should we split our time with somewhere on the east side of Crete, maybe Agios Nikoklaos or Ierapetra? This is our first time ever visiting.

When we were planning our trip to Crete for two weeks our Greek friends convinced us to focus on western Crete. We stayed in Chania except for a short trip to Loutro on the south coast. We went new places almost every day and wished we had more time. The weather in early October was sunny and warm, not hot. The numbers of tourists had dwindled too. We were in Greece for a month and put Crete at the end.

I don't think the difference in temps during your stay is worth changing... and frankly for a 5 night stay would NOT do the long drive to Ag Nik or south to Ierapetra. Too many glorious discoveries in western Crete which does have the most wonderful landscapes of the island .... at the other end there are some specific archeological sites (GOurnia, Zakros) that attract the dedicated Minoan-history specialists, but u haven't mentioned that. leave that until you've been to Crete a few more times!

I was on Crete for 10 days the first half of October and based myself in Chania.

The weather was still very nice, mild temps, short sleeve during the day and some nights and an occasional light jacket at night. Some rain but no wash outs.

However, there is no guarantee regarding the weather so be prepared for anything.

With just 6 days pick one location and use it as a base.

Six days is just a drop in the bucket for Crete but at least it will give you a "taste" of the lovely island and hopefully the next time you go you can add many more days as it will take weeks to fully enjoy and experience.

You are correct about the weather at that time of year. It is slightly warmer on the south coast however you are still close to mountainous areas which tend to have more cloud.
e.g. if you want to hike the Samaria gorge in mid October chances are slim due to increased possibility of rain in the White mountains.

I have stayed in Chania, Paleochora, Loutro, Frangokastello, Plakias, Matala in the west half of Crete, that took over 3 weeks.

Essentially you only have 4 days, a small sample trip, so not enough time to split with the Ag. Nikolaos/Ierapetra area.