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There are a number of possible factors so I won't try to guess on what the cause would be. I'd recommend utilizing X-Ray tracing on API Gateway and your lambdas. This will give you insight into where the time is being spent and some hints as to what might be going on.
Some resources to get started on getting AWS X-Ray integrated:
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I don't feel like this answers the question. The scenario is pretty simple, and I have yet to get a clear answer on this. I have an API Gateway and an AppSync API both in the same region, both with the same Lambda functions hooked to them, both with requests coming from the same place. API Gateway is always significantly faster. I really want to use AppSync, but the performance is unacceptably slow.