Which measure should be used in a PCA or RNA-seq data? TPM or counts?
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 rlog and vst, this seems likely), then please go ahead and use rlog or 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).