Here's a Python-based approach:

#!/usr/bin/env python

import sys

d = {}
r = []
c = []

for line in sys.stdin:
    (row, col, val) = line.strip().split('\t')
    if row not in d:
        d[row] = {}
        r.append(row)
    if col not in d[row]:
        d[row][col] = val
    if col not in c:
        c.append(col)

sys.stdout.write("\t%s\n" % ('\t'.join(c)))
for row in r:
    nr = []
    for col in c:
        try:
            nr.append(d[row][col])
        except KeyError:
            nr.append('??')
    sys.stdout.write("%s\t%s\n" % (row, '\t'.join(nr)))

Then:

$ ./condense.py < data.txt
        SNP_1   SNP_2   SNP_3   SNP_4
ind_1   AA      AB      AA      ??
ind_2   AA      AA      ??      ??
ind_3   AB      AA      AB      AA