Hi,
Yes that looks like Alice is sister of John. I have baptism cert for John (1856) that my grandmother kept, from St Audoen's church, so i'm sure you'll find Alice's there.
I had attached link to census of Thomas from 1901 and he was living at that time in Jervis street with his sons. He died 2nd January 1902 and that address is on his grave at Glasnevin. He's buried with wife Catherine, who died 12 Dec 1882. Also buried with son Thomas (Alice brother), d 1941.
Catherine is originally from Bagenalstown Carlow and Thomas from Clonmel Tipperary. Thomas moved to Dublin during the famine.
So far i know Catherine and Thomas had sons, John, Thomas, Michael, daughter Catherine and now Alice. You have mentioned Mary as well.