The question and reply don't match. It should be:-A: Whom do you think will come here first?
B: It could be John.
A: Whom do you think will come here first?
B: It will be John.
B: It won't(will not) be John.
C: Whom do you think will come first?
D: I don't know. It may be John, though.
E: Could that be John coming first in the race?
F: I am not sure. It could be John.
F: It couldn't be John, for sure!