The word "sapinda" is derived from the word "pinda" a rice ball. Pindas are offered to ancestors as obsequies. Two persons are sapindas if their ancestors are the same. Among Hindus pindas are offered to ancestors only on the patriarchal lineage and not on matriarchal lineage. Sapindas will belong to the same gotra and sagotra marriages are prohibited up to any number of generations. Hindu Marriage Act limits it up to 5 generations. Many persons may not know even their 5th generation cousins.
Though one offers pindas only to ancestors on the father's side, one performs obsequies to one's own dead mother also. When one offers pindas to one's dead father, fore-fathers up to a few generations upwards are also counted. If father is dead but mother is alive, patriarchal ancestors of the living mother are also counted. That may be the reason why marriage is prohibited between sapindas on the mother's side also. In any case among most communities in India marriages between first or even second parallel cousins on the mother's side is prohibited even when they belong to different gotras.
In your case your mother and the boy's mother are cross cousins. Hindu Marriage Act is silent on the permissibility of marriages between cross cousins and still less on the further descendants. In North India marriage between first cross cousins in prohibited. But in Maharashtra and further South such marriages are allowed.
I feel that as you are only children of first cross cousins, you can go ahead and marry your second cross cousin. There is no law to prohibit that, to the best of my knowledge.