The basic difference
Binaural beats rely on presenting different tones separately to the ears so that the listener perceives a beat. Isochronic tones use obvious periodic amplitude changes—a sound turning on and off or pulsing—so the rhythmic modulation exists in the acoustic signal itself.
Headphones
Headphones are central to standard binaural-beat delivery because they preserve the separate left/right tones. Isochronic pulses do not require the same ear-specific frequency difference, although headphones can still be useful for isolation and comfort.
Do we know which is better?
There is no defensible universal answer that one format is “better for the brain.” Effects depend on the research question, implementation and outcome. Treat categorical superiority claims cautiously unless they are tied to a specific well-designed comparison.
Practical choice
Choose based on whether you enjoy the sound, whether headphones fit your setting, and whether the recording supports your intended routine. For focus, compare either format against simpler options such as instrumental music or steady noise.