I'd also say go via Athens. Several connections available to both Chania an Heraklion. Personally, I'd go AB to Heraklion.

Even though the place I sometimes rent is nearer to Chania, it's not that bad a drive along the coast from Heraklion as long as you don't get flustered by Cretan drivers completely ignoring road markings and traffic signs.

If you must go direct Monarch is probably sufferable, especially if you buy the extra legroom option, although I'd still prefer going BA/AB via ATH, and getting some TPs in the process