tldr: log transform counts and TPMs, but rlog/vst are preferred
TPM should be log transformed to get more useful results. If you're using DESeq2 already (given the reference to
vst, this seems likely), then please go ahead and use
vst. That will give you more reasonable results than raw counts. If you're stuck with counts for some reason, then first use normalized counts so they're at least a bit more comparable and then log transform them so your highly expressed genes aren't driving everything.
Edit: As an aside, if you know what the batch effect is (e.g., library prep. date), it's sometimes convenient to include that in your model. You can then assess the genes that are actually changed due to that, which is sometimes handy to know (e.g., which genes might be more/less prone to degradation).