しかし僕だけではなく、もうひとり—いや、もう一匹の珍客がいたらしい。

、—、。

But it seems it wasn't just me — there was another guest, or rather, another animal.

Literal

However I [only-だけ-ではなく], one-more person — no, one-more [counter-for-animals-匹] [gen-の] rare guest [subj-が] existed [seems-らしい].

しかし 'however' is the formal written 'but.' だけではなく 'not only X but...' is the additive negation frame, a common written construction. 一匹 uses the counter 匹 for small animals (versus 人 for people) — the speaker pauses with 'no' to correct 一人 to 一匹, comically revealing the 'other guest' is an animal. 珍客 'unusual / rare guest' is a formal literary compound.