I would answer kindly as if the question would not be awkward or obvious. Like "Yes, it's just me".

I would instead avoid sarcastic answers as "Yes, it's just me, as you can see, unless you've just became blind".

This is because people sometimes makes such questions just to start a conversation.

And... if I may... it seems to me that you are a little bit too strict in interpreting someonelse's question. Your manager asked you "You're the only one here?". And I would guess, from your question, that you maybe though "I'm obviously the only one here. You can see that. So why bother to ask?". But maybe some colleague of yours just left the room to answer an incoming call, maybe another one paied a quick visit to the toilet. How could she/he know  ?

I would answer kindly as if the question would not be awkward or obvious. Like "Yes, it's just me".

I would also avoid sarcastic answers as "Yes, it's just me, as you can see, unless you've just became blind".

This is because people sometimes makes such questions just to start a conversation.

And... if I may... it seems to me that you are a little bit too strict in interpreting someone else's question. Your manager asked you "You're the only one here?". And I would guess, from your question, that perhaps you thought "I'm obviously the only one here. You can see that. So why bother to ask?".

But maybe some colleague of yours just left the room to answer an incoming call, maybe another one paid a quick visit to the toilet. How could she/he know?