How to filter info score post-imputation?
In simple GWAS setups, each SNP is analyzed independently.  In those cases you can filter out SNPs with poor INFO scores at any point.

For analyses that combine information across SNPs (for example FaSTLMM), I would recommend filtering out SNPs before running the step that combines information across SNPs.

So, if you filter right after running Impute2, you should be safe.