I am looking for an alignment tool that is good at aligning a lot of small amplicon sequences to small reference sequences.
I have tried BWA and Bowtie, (and BLAST with a makeshift Perl parser behind it) but can someone point me to another good alignment program for this kind of job?
I just saw this question, so I'm not sure if you've figured the issue out or not. I'm not sure how long your reference is or how long your amplicon sequences are, or how much variability you see in the amplicons.
I've recommended Julian Catchen's Stacks pipeline to numerous people here already. I'm using it to address population genetic questions with metagenomic amplicon data, but depending on what you are actually doing perhaps our uses aren't very different. Give it a try and see what you think. You'll need to know a bit of MySQL and be confident working in the shell to use it. I generally use the genotypes command in the pipeline and if you read the documentation you can specify which flags to use for that command that will be specific for your data.