When Agent Neville calls "Hey, Singer!" it's a double reference. The actor playing Agent Neville is played by Jim Beaver, who played Bobby Singer on Supernatural. Bobby Singer is named after producer Robert Singer, who worked alongside Timeless' co-creator and Supernatural's creator, Eric Kripke.
When he first meets Eliot Ness, Wyatt gave him the aliases for the team of "Connery", "Costner" and "De Niro". The real Sean Connery, Kevin Costner, Robert De Niro starred together in The Untouchables (1987) portraying Jim Malone, Eliot Ness and Al Capone, respectively.
Lucy asks "Don't you think it's because you want to set right what Al had done wrong?" This is a nod to another time travelling TV series, Quantum Leap (1989). Part of the opening narration of Quantum Leap is, "striving to put right what once went wrong." In Quantum Leap, one of the main characters is named Al Calavicci.
Rufus chuckles that he feels the three are very 'untouchable'. Lucy says, "Oh boy!" Sam uses this line in almost every "Quantum Leap" episode.
Supernatural s7 ep 12 "Time After Time" had Dean meeting Eliot Ness in 1944. Both shows are created by Eric Kripke.