The Tottenham and Leicester City stars lead the Premier League scoring charts with 22 and 19 goals respectively, with Rooney having amassed only 11 in the top flight since December 2014.
But Van Gaal is adamant that the 30-year-old - who is nearing a return after two months on the sidelines with a knee injury - remains England's leading centre forward.
"It always depends on their form because everybody has tendencies in their shape," the Dutchman responded when asked whether Rooney was still England's best striker.
"It is always like that. Wayne is more like that. Normally he is the best striker, but Harry Kane, how many has he scored? That also counts for a striker and also for Wayne.
"So, it’s also dependable on your team, how they are playing, so you cannot say that so easily. But when you see his record he is the best striker.”
United travel to White Hart Lane to take on Tottenham this weekend, with the Red Devils currently a point behind Manchester City in the race for the top four.
Van Gaal acknowledged Kane's importance to Spurs but insisted his side could not focus solely on the goalscorer.
“I cannot remember that he [Kane] scored [against us]," he told reporters. "When I say that I am challenging him also, so it’s not so smart of me.
"But we are never defending against just one player. We defend like a team and we defend the attack of Tottenham.
READ MORE | Darmian: Top-four finish a must
“We have analysed them. Of course, Kane is very important but [Christian] Eriksen is also very important and Dele Alli is also very important.
"I can start with [Hugo] Lloris because he makes very quick set-plays and also [Toby] Alderweireld has a very good pass, so it’s the team you have to solve and not only Harry Kane.”
Rooney is unavailable for Sunday's trip to the capital, but could return for Wednesday's FA Cup quarter-final replay against West Ham United.
Van Gaal refused to confirm whether his captain would be involved but says he does not expect Rooney to require too much time to get back up to speed.
“That you can never predict [his availability for West Ham], because you have to see if everything is going well," the 64-year-old said.
"He has only trained two times with us and you cannot predict how his injury evolved. We have to wait and see and I have to see the Under‑21 game against Middlesbrough [on Monday].
“So I cannot say that because he can be so good that I shall be forced to give him a position in the team. But it depends on what we see and today was another day. Tomorrow also.
"Let’s wait that he plays 60 minutes at a lower level and then he can play against West Ham United, you never know.
“I cannot say that [it will be a while until he returns to his best] because when I saw him training [on Thursday], for example, he scored a goal, he made a fantastic chip over the goalkeeper. It was his first training session and I said to him, ‘I have never seen that this season’."