We are currently in Heraklion and just got done with a speedy tour of the museum and Knossos since even our hotel had the times wrong. The Museum is only open until 15:00 (17:00 on MONDAYS only!). Knossos is open until 17:00 and it seems they are strict with kicking you out on time. Even our hotel didn't know the times - they told us us the museum was open until 5:00 pm - we almost missed it all together! I would recommend 2 hours for the museum and 2 hours for the site.
Since we were so late and didn't have time to dawdle we got a guide and enjoyed it (although it was a little pricy). You probably could get the same from a good guidebook but it also depends on the personalities of the people in your group - my boyfriend would have zoned out it I had try to read to him from a guidebook but he enjoyed the guide. I will say arriving at 3:00 was wonderful in terms of crowds. We pulled up to the lot right next to the entrance and the crowds were very light inside. Yes a lot of it is recreation - and one person's interpretation - but lots of archeology is theory and supposition anyway- for us, it helped us to see what might have been and kept our attention.
I loved the museum and had wished we had more time - but I'm happy we didn't miss it all together. The pieces are amazingly "modern" and have wonderful detail. If your are not a museum person and/or only lightly interested - you can actually walk through it in an hour. If it works out, I would recommend the museum first and then the site.