To solve this problem, let's analyze each option step by step:

A: $-4^0=1$

- The operation $4^0$ equals $1$, but since there is a negative sign without parentheses, it's actually $-(4^0) = -1$. So, A is incorrect.

B: $x^6\div x^2=x^4$

- According to the laws of exponents, when dividing powers with the same base, we subtract the exponents: $x^6 \div x^2 = x^{6-2} = x^4$. So, B is correct.

C: $(-3)^{-1}= \frac{1}{3}$

- The operation $(-3)^{-1}$ equals $\frac{1}{-3}$, not $\frac{1}{3}$. So, C is incorrect.

D: $(-a^2b^3)^2=a^4b^9$

- When squaring a product, we square each factor inside the parentheses. However, the negative sign also gets squared, which makes it positive. So, $(-a^2b^3)^2 = (a^2)^2(b^3)^2 = a^{2*2}b^{3*2} = a^4b^6$, not $a^4b^9$. So, D is incorrect.

Therefore, the correct operation is:

$\boxed{\text{B}}$