I'm not so sure. Just as Science bootstrapped itself, I don't see why there couldn't be a new method that could work completely independently.
But how would we
know that it worked, if not by comparing what it told us to the facts?
Let's suppose that someone comes forward and says that he can perform psychic remote viewing. "OK," we say, "I'll go into the other room, and you tell me what I'm doing." If he can do that, then we have verified his psychic sense scientifically, just as we can verify my more mundane powers of sight and hearing.
But suppose he replies, "Ah, my method only works on planetary surfaces no nearer to us then the Andromeda galaxy. Let me tell you the freaky things the aliens are doing over there." Suppose, moreover, that he was telling the truth. Then we wouldn't
know that he was telling the truth, because we'd have no way of telling whether he really did have this power or was merely making stuff up. He himself, if he was honest, wouldn't know whether he was really capable of remote viewing or just of inducing complex hallucinations in himself.
I could perhaps think of a better and more rigorous example if I thought about it a bit longer, but you see what I'm getting at?
Science does not, after all, really "bootstrap" itself, it is not a closed system of thought. It ascends not by tugging on its own bootlaces but by climbing laboriously upwards from the level plain of our qualia.