The public buses from Ag. Nikolaos to Heraklion that come in question for you leave at 9:00, 9:30 and 10:00, and the trip is less than 2 hours long. There is a less than one km long walk (uphill!) from the harbour to the bus station, so I'd suggest a cab. Knossos and the Museum may be too much, info-wise the latter is more worth it than the former (nice setting, but Sir Evans' ideas of how the palace looked are a bit Disney-like by today's archaeological standards). When in Heraklion, get a cab to/from Knossos or walk (uphill) to the museum (10 min. from the bus terminal). If you want to be certain that you'll reach your bost in the evening, I'd suggest you take the 16:45 or 17:45 bus back.