Μέγα μέρος όν

Can one use Μέγα μέρος όντα instead of Μέγα μέρος όν in Thuc. 5. 32.3

No. μέγα μέρος is neuter, so the participle has to be neuter too. όντα is masculine, όν is neuter.

καὶ Κορίνθιοι καὶ Ἀργεῖοι ἤδη ξύμμαχοι ὄντες ἔρχονται ἐς Τεγέαν ἀποστήσοντες Λακεδαιμονίων ὁρῶντες μέγα μέρος ὂν .I think the part should agree with Tegea as its subject not with the predicate noun which is μέρος .

Tegea is fem not masc.
No doubt Thuc cd have phrased it differently and used the fem pple (and αυτην) but after μεγα μερος he stuck to the neuter.

I think you are right.