He, together with they/them, is going to church.

if you are asking whether to use they or them, these words are pronouns, not prepositions, and the answer is them.

Thanks, contrex.

Indeed, they are pronouns. Mistake noted.

I know this was not your question, but there is something else incorrect in your example. The word "is" should be "are". More than one person or plural would use the word "are".

Strictly speaking, no. X, along with, together with, as well as (etc) Y should take the singular if X is singular. It is true that many native speakers ignore this.

Consider "beauty as well as love is redemptive". The 3rd person singular verb-form is indicates that the subject is singular: is agrees with beauty, so that as well as love is treated syntactically as an adjunct, not as a coordinate.

See The Cambridge Grammar of the English Language (p.1316).

Also:

The title as well as the tone of this volume errs, perhaps, in being unduly modest.

The title, as well as the tone, of the novel derives from Lady Molly Jeavon's household.