Prophet of Kruphix: Can I flash Bestow?
Yes, you can, for both. Prophet of Kruphix allows you to cast "Creature Cards" as though they had flash. Thassa's Emissary IS a Creature Card. It's NOT a "Creature", as a "Creature" is a permanent on the battlefield, which it isn't while it's in your hand or on the stack. But it IS a "Creature Card", and that's all that matters.

See rules for Bestow, noting that Bestow ability that allows you to cast it as an Aura is a static ability of the card itself, not of a creature or aura permanent.


  702.102. Bestow
  
  
    702.102a Bestow represents two static abilities, one that functions while the card with bestow is on the stack and another that functions
    both while it's on the stack and while it's on the battlefield.
    "Bestow [cost]" means "You may cast this card by paying [cost] rather
    than its mana cost." and "If you chose to pay this spell's bestow
    cost, it becomes an Aura enchantment and gains enchant creature. These
    effects last until one of two things happens: this spell has an
    illegal target as it resolves or the permanent this spell becomes,
    becomes unattached." Paying a card's bestow cost follows the rules for
    paying alternative costs in rules 601.2b and 601.2e–g.