Only "kio" is correct here. "kion" would be wrong.
"kio" is used as a relative pronoun here, so it's part of the relative clause. While that "kio" refers back to "ĉion" (which is the direct object of the main clause and thus bears the "-n" marker), within the relative clause, it acts as the subject (of the conjugated verb "estas"), so it cannot bear the "-n" object marker (i.e., it cannot be in accusative case).
By the way, while the comma rules of Esperanto might not be formally fixed, it's so usual in Esperanto to delimit relative clauses with commas, that omitting it seems wrong to me here. Thus, I'd write that as
Mi ŝatas ĉion, kio estas sur la tablo.