Highlights of Heraklion, Crete?

I went last year for 2 days. My husband and I were thrilled to go to Knossos and to visit the Archeological Museum. This took us several hours (more than 2, possibly more time than you will have). We also went to visit the restored Venetian fort--which we found very interesting (and cheap!); we probably spent an hour there. I had read about the Heraklion Historical Museum, but we did not have time to go. If you just want to walk, the area around the Morosini fountain was interesting. We enjoyed a nice walk along the sea wall (passing the fortress).

Knossos and the Archaeological Museum are the two outstanding sights of Heraklion. I would get a guide for Knossos. There are some available at the entrance. It really helps to understand what you are seeing. I believe they charge €80 for up to 8 people. When we were there, there were no other people wanting a tour in English, so we paid the whole fee ourselves. At €40/pp it was still a bargain compared to the prices we had seen on line for private tours

Both Rebecca and Rosalyn are spot on with their advice. I found it helpful to visit the museum before going out to Knossos. You really need 2 nights though unless you have a private transfer to Heraklion in the morning. I took the bus and the scheduled 2 hour trip took nearly 4 hours. Allow at least 2 hours for the museum and 5-6 hours for Knossos, including the bus there and back (and some wait time - if you aren't near the front of the line, you may be standing for much of the ride.

Knossos and the museum are highlights in Heraklion. But don't overlook the central area of Heraklion. There is the Venetian area at the harbour plus the Castello fortress. There is a very nice area in the center with old buildings it is also where the locals head out for the evening promenade.

Here is what central Heraklion is like.
Heraklion https://www.flickr.com/photos/stanbr54/sets/72157655935354556
Castello https://www.flickr.com/photos/stanbr54/albums/72157686964935102

I was in Heraklion in October 2018. I was there for only one night and 1-1/2 days. I went to Knossos and then the archaeological museum, in one day. The next day I had time for the Crete historical museum and the Koules fortress. As time allows, in order of most to least importance I would see Knossos, the archaeological museum and the fortress; the average person not that into less popular museums can skip the Crete historical museum. If there is extra time you can see the old city walls and walk past the reconstructed Venetian style city hall.