The Better Reader is an online reading program marketed by McGraw Hill. It’s not specifically geared to English Language Learners, but Intermediate and Advanced students might find it useful.
It appears you have to purchase the program to access all of the exercises, but there are quite a few exercises that can be done in the free “Demo” portion. The site has three sections: Reading Comprehension, Vocabulary, and Reading Efficiency. You have to complete a registration process to access the demo, but it only takes a few seconds to complete.