Thus, then, in our hearts’ honeymoon, lay I and Queequeg – a cosy, loving pair.
This type of "intimacy" and I say that term loosely among guys in the 19th century was not uncommon. It was more of a very close/trustful friendship. Abe Lincoln was known to have shared a bed (not in a sexual sense) with another male while setting up his law practice.
the great flood-gates of the wonder-world swung open, and in the wild conceits that swayed me to my purpose
World was still a large place to people there and those seafaring peoples had plenty of wonder about the world. To me "the great flood-gates of the wonder-world swung open" once a ship left port.
and, mid most of them all, one grand hooded phantom, like a snow hill in the air.
This is clearly a reference to the white whale. Reminds me of the numerous times the white whale was seen in the movie "In the Heart of the Sea".