Bowen, top scorer for the Premier League side this season, missed the 2-0 loss in Germany along with the defeat by Fulham at the weekend with a knee injury, but has returned to training and is available for selection.
"It was great to see Jarrod out there, first time we had him back, so we're not sure about him," Moyes told a press conference ahead of Thursday's tie.
"I would never risk any players if I thought they had a chance of injury or it wasn't right, player's welfare is the most important thing.
"But you always want your best players back in, obviously I want goalscorers back in as well, and Jarrod has been that for us this season. Everyone knows what Jarrod has done for us, so if he's back that will give us and the crowd a big lift."
Moyes said that Bowen's selection will be a late call, along with midfielder Kalvin Phillips and goalkeeper Alphonse Areola, who were also missing in the first leg.
West Ham lost to two late goals away to Leverkusen, and Moyes is prepared to wait as his side attempt an unlikely comeback.
"We went to Leverkusen and got to the 83rd minute before they scored their first goal. It might take us that long, we have to be patient, and play until the end," he said.
"You never know how those games are going to go. We did a good job on them in the first leg but it was still not enough. We tried very hard last week and we will try very hard tomorrow."
Leverkusen, on a 43-game unbeaten run across all competitions this season, won their first Bundesliga title on Sunday, and West Ham will be hoping their celebrations have taken their toll.
"It's fantastic they won the league and they should celebrate something like that," Moyes said.
"Let's hope that they have had a few of those big German beers."
