PCA before Affinity Propagation (AP)
Independent of the number of features, you will obviously need much more than

3 * 100.000 * 100.000 * 8 bytes

of ram (with double precision floats). That is 240.000.000.000 or about   240 GB. Not only is this a lot of RAM to have, but AP will have to do many passes over this RAM, so this will take forever, even after computing the distance matrix.

So clearly PCA won't help. You just cannot afford an algorithm with O(n²) memory and O(n²) runtime. PCA reduces d, but the runtime of AP itself does not depend on d.