That is one of those dilemmas we always fight with.
Eighter you accept the Y branch and get a nice tree with a nice canopy with one flaw in short time. Or you cut one of the branches and start to build a new canopy. That will give you a better tree but will take longer time.
I dont think Y branches is that bad on Apple trees. After all we are aiming at a miniature of an old tree. Crabapples often have Y branches. I would go for option one and think of it as a feature, not a flaw.
this is an old picture.. I'm in Germany.. I've thought similar... as neither of the two Y branches is in a position to become a new leader without some good bending... I'm going to see if I need to move it to a different container next year, and if not.. do a good hedge prune in the winter...
OK, seriously, I see no problem with the Y shape. There are lots of trees in nature with that shape, and lots of apple, cherry, etc. In fact, I have two cherries and a pear tree in my yard, growing naturally with a Y shape.
What I would do is cut a couple of branches off down close to the fork of the Y shape, and prune the rest back to make a reasonable canopy shape, depending on what the branch structure looks back - this means in the winter without all those distracting flowers and leaves.