complex object

They both mean the same thing, both would be correct if the first word was capitalized. The first sentence is the better choice.

My sister doesn't want me to help her.

I would go further than Lewis, and say that My sister doesn't want me to help her is the correct sentence.  In English, some verbs can naturally be followed by not to + infinitive, and others cannot. Want, like, dislike, and hate, and probably other verbs are grammatically expressed, on the other hand, by the do + not + verb pattern.

There is a complicated taxonomy of English verbs out there, usually only understood by linguists, if at all, and I am certainly not fluent in it.  But My sister wants me not to help her sounds awfully incorrect to my ear, compared to My sister doesn't want me to help her.  On the other hand, a sentence like She wants me to try not to be rude makes perfect sense, and has a completely different meaning from He asked me not to try to climb Mt. Everest.

As I compose this entry, myriad exceptions and examples are swirling through my mind.  My insistence--that My sister doesn't want me to help her is correct, whereas My sister wants me not to help her is not--remains unwavering, but I look forward to other opinions, especially those that uphold my intuition. 

But what about the song "I want you not to go"?