Rashi on I Samuel
Eili thought she was drunk. Because they were not accustomed to praying silently.
Metzudat David on I Samuel
And Channah: But, "Channah was praying in her heart" - meaning to say, in a whisper, as if she was speaking to her heart, so it was not audible to Eli.
Radak on I Samuel
Spoke in her heart: It is like its translation [in Targum Yonatan], "she prayed in her heart." Meaning to say, she concentrated [with] her heart in prayer.