To answer your question I will draw an analogy with a simple question about classical mechanics. Hopefully this will clarify the confusion.
Imagine someone coming to you asking what is the correct expression for acceleration. Somewhere she read the correct expression was:
$$a=\frac{\partial^2 x}{\partial t^2}$$
Somewhere else she read
$$a=\frac{F}{m}$$
She is wondering, which of these two is the correct expression. My answer would be that the first expression is the definition of the acceleration, while the second expression is the value acceleration might take in a given experiment. The equation of motion is thus:
$$\frac{\partial^2 x}{\partial t^2}=\frac{F}{m}$$
The question you are asking is similar.
$$\hat E =i\hbar \frac{\partial}{\partial t}$$
is the operator that is defined as the energy operator, while
$$\hat H = \frac{-\hbar^2}{2m}\nabla^2 +V$$
is the energy operator for a given experiment. The equation of motion is thus:
$$i\hbar \frac{\partial}{\partial t}=\frac{-\hbar^2}{2m}\nabla^2 +V$$