Besides the G Suite for Nonprofits Google also makes available G Suite for Nonprofits Business and G Suite for Nonprofits Enterprise which are actually just discounts on the regular Business and Enterprise products rather than the distinct G Suite for Nonprofits. I believe with these you can select the location of data storage.
Even if the data is stored in the EU, Google (or Microsoft for that matter) does not guarantee that data cannot be accessed from the US. That makes sense, since most of their operating staff is probably based in the US, but does mean that it is not GDPR-compliant, no matter what Google says about that. Google states that they are using the SCCs now Privacy Shield has been invalidated, but as Google US is an entity under reach of FISA I highly doubt that they can provide the necessary safeguards required under the GDPR and the SCCs.