Laguna Shores sits on the cliff's above the beach and gets good reviews.
San Clemente Cove is directly across a very small street from the San Clemente Pier...effectively at the beach...but not on it.
Many of the resorts south of Laguna Beach through Solana Beach (Winners Circle) are located across the street from the beach or within a block, are also near the train tracks where Amtrack makes several trips daily between San Diego and LA, and as such you get the noise of the train. Even louder still are the state campgrounds which sit at the beach. San Clemente Inn, where we own, is not on the beach but a medium to long one block walk to the beach. There are bluff's and a state park between the tracks and SCI which blocks out train noise, a definite plus.
Laguana Shores has no train tracks anywhere nearby most likely matches what you are after.