Hi Tenir,
It depends on what you're trying to say. If it's a greeting or a wish, then "God bless you" is fine. If it's a statement, like "Rain falls," then "God blesses you" is correct.
Technically, if you are saying "I pray that God bless you" it's the subjunctive mood, so it doesn't take the -s you usually see with the third person. Otherwise, if you say "God blesses you every day," it's a statement, so you include the s at the end of the verb.
Hope this helps!