There can be a significant difference in the meaning between the two sentences, depending on context.
I've heard a noise in the kitchen. I had better go to check.
I'm standing somewhere other than the kitchen, and I've heard a noise that originates from the kitchen.
I've heard a noise from in the kitchen. I had better go to check.
I'm standing in the kitchen, and I've heard a noise that originates from somewhere else.
Whether they mean the same thing or not is entirely dependent on context. Either they mean the same thing, or they mean something completely different. The two sentences along don't give enough detail to say what's actually being described.
Where are you standing? Where is the noise coming from? Unless you can provide the missing details, it's not possible to say which preposition is better.