Who does he like to play with? [best choice]
Whom does he like to play with? [very formal]
With whom does he like to play? [very formal]
"who he likes to play with ...." as it stands cannot be a direct question because it has no auxiliary verb to form the interrogative. However, it could be used as an indirect question:
"she doesn't know who(m) he likes to play with, but ...."
Whom sounds a bit too formal, but not grammatically wrong.
It would be WRONG in the following instance to use the auxiliary verb:
"she doesn't know who(m) does he play with ...."
because this is an indirect question and the auxiliary verb 'does' is not required in indirect questions.