Is it permissible to give charity to the poor who sit at the doors of mosques or shops, or is it preferable to give charity through donation boxes?

It is best to give charity where its reward is maximized, specifically to those in greater need than others. If it is highly probable that the seated beggars are in dire need, then it is better to give charity to them. If the charity is intended for what it is dispensed for through collection boxes, then it is better to designate them for the charity. Combining both approaches is even better.