Hi Qiimer,
Yeah, there's some great packages out there. I use phyloseq (phyloseq: Explore microbiome profiles using R). I think there is also a community tutorial within the qiime2 docs about performing data analysis in R, which probably contains great suggestions on other packages also (Tutorial: Integrating QIIME2 and R for data visualization and analysis using qiime2R). I haven't used qiime2r (sounds pretty great!), but I know that phyloseq allows you to import and work with .biom tables.
Hope that helps!
Mark