tl;dr
Use basenc(1) from coreutils:
$ printf "xs?>>>" | basenc --base64
eHM/Pj4+
$ printf "xs?>>>" | basenc --base64url
eHM_Pj4-
As with base64(1), add the -d switch to decode.
A bit of explanation
Recent versions of coreutils include basenc(1) which supports several different encodings. From its help screen:
--base64          same as 'base64' program (RFC4648 section 4)
--base64url       file- and url-safe base64 (RFC4648 section 5)
--base32          same as 'base32' program (RFC4648 section 6)
--base32hex       extended hex alphabet base32 (RFC4648 section 7)
--base16          hex encoding (RFC4648 section 8)
--base2msbf       bit string with most significant bit (msb) first
--base2lsbf       bit string with least significant bit (lsb) first
--z85             ascii85-like encoding (ZeroMQ spec:32/Z85);
                  when encoding, input length must be a multiple of 4;
                  when decoding, input length must be a multiple of 5
Here is a string that illustrates the difference:
s="xs?>>>"
As binary:
$ printf "%s" "$s" | xxd -b -c1 | cut -d' ' -f2 | nl
     1  01111000
     2  01110011
     3  00111111
     4  00111110
     5  00111110
     6  00111110
And as 6 bit blocks (as base64 reads the data):
$ printf "%s" "$s" | xxd -b -c1 | cut -d' ' -f2 | tr -d '\n' | fold -w6 | nl
     1  011110
     2  000111
     3  001100
     4  111111
     5  001111
     6  100011
     7  111000
     8  111110
Note that block 4 and block 8 map to / and + respectively (Base64 table on Wikipedia):