Let's Encrypt currently issues 4096 bit RSA certificates if requested (default, however, is 2048). But its parents, intermediate "Let's Encrypt Authority X3" and root "DST Root CA X3", are both 2048 bit.
According to this thread, the well-known Qualys SSL Labs test gives a setup with 4096 bit Let's Encrypt certificate a better rating (in "Key Exchange" section) than to 2048 bit one. Why? Isn't a certificate chain as weak as the weakest link?