I think both sentences are technically correct, though to my ears they don't sound quite natural for casual speech. Both are equivalent in meaning I think, as the end result is the same - he's not going to help you as far as you can tell.
In casual speech, I might include the word 'like' in each sentence:
It seems like he's not going to help me.
It doesn't seem like he's going to help me.
Because both of these sentences are written using more casual English, I substituted the contraction he's for he is, but this perhaps is a personal choice and depends on when and where you would use these sentences.