It's about a man who ends up on a space whale that can "dive" through time, he picks up a capsule with a woman in stasis that he is attracted to, he also saves a little girl who he travels through time with, I forget most of the story but in the end the little girl ends up being the woman in the stasis capsule. I swear the main characters name is jon starflyer or something close to it. A man and a little girl in a space whale
It sounds like you read either part of the Spacewhale series of stories by Robert F. Young, or the novel Starfinder (1980) which is apparently the same series just collected together in a single volume.
You can read the first book of the series online: the hero is called Jonathan Sands (close enough to Jon), and he ends up on - swallowed by, in fact - a gigantic space whale which has the ability to travel through space and time. I couldn't find much detail online about any of the stories in the series beyond the first one - although I did notice that one of them is entitled As a Man Has a Whale: a Love Story, which could be what you're looking for - but I did find this description of the novel (emphasis mine):
John Starfinder had hunted the spacewhales as they plunged beneath the surface of the space-Time sea, plummeting into the past & resurfacing light years away, he had killed the whales & made them ready as spaceships. But one day a captive whale spoke to him, begging release, promising power. And in one bold gesture, Starfinder threw over his old life to escape w/the whale. Together they rode the vast expanse of ebony space--to the beginnings of time & back again--until a new call, the love of a dead woman, led him to the most difficult & daring venture of his life--the ultimate challenge of a headlong struggle with death.
That's GOT to be what you're looking for.