There are four different sects of Vaiṣṇava ācāryas—the Śuddhādvaita, Viśiṣṭādvaita, Dvaitādvaita and Acintya-bhedābheda. All the Vaiṣṇava ācāryas in these schools have written commentaries on the Vedānta-sūtra, but the Māyāvādī philosophers do not recognize them. The Māyāvādīs distinguish between Kṛṣṇa and Kṛṣṇa's body, and therefore they do not recognize the worship of Kṛṣṇa by the Vaiṣṇava philosophers. Thus when the Māyāvādī sannyāsīs asked Lord Caitanya why He did not study the Vedānta-sūtra, the Lord replied, "Dear sirs, you have asked why I do not study Vedānta, and in answer to this I would speak something, but I am afraid that you would be sorry to hear it."
"We shall be very much pleased to hear You," all the sannyāsīs replied. "You appear just like Nārāyaṇa, and Your speeches are so nice that we are taking great pleasure in them. We are very much obliged to see and hear You. Therefore we shall be very glad to hear patiently and accept whatever You say."
The Lord then began to speak on Vedānta philosophy as follows: Vedānta-sūtra is spoken by the Supreme Lord Himself. The Supreme Lord, in His incarnation as Vyāsadeva, has compiled this great philosophical treatise. Since Vyāsadeva is an incarnation of the Supreme Lord, he cannot be likened to an ordinary person, who has the four defects which arise due to contact with material existence. The defects of a conditioned soul are: (1) he must commit mistakes; (2) he must be illusioned; (3) he must possess the tendency to cheat others; and (4) all his senses must be imperfect. We must understand that the incarnation of God is transcendental to all these defects. Thus whatever has been spoken and written by Vyāsadeva is considered to be perfect. The Upaniṣads and Vedānta-sūtra aim at the same goal: the Supreme Absolute Truth. When we accept the import of Vedānta-sūtra and the Upaniṣads directly as they are stated, we become glorified. The commentaries made by Śaṅkarācārya, however, are indirect and are very dangerous for the common man to read, for by understanding the import of the Upaniṣads in such an indirect, disruptive way, one practically bars himself from spiritual realization.
According to the Skanda and Vāyu Purāṇas, the word sūtra refers to a condensed work which carries meaning and import of immeasurable strength without mistake or fault. The word vedānta means "the end of Vedic knowledge." In other words, any book which deals with the subject matter indicated by all the Vedas is called Vedānta. For example, Bhagavad-gītā is Vedānta because in Bhagavad-gītā the Lord says that the ultimate goal of all Vedic research is Kṛṣṇa. Thus Bhagavad-gītā and Śrīmad-Bhāgavatam, which aim only at Kṛṣṇa, are to be understood to be Vedānta.
In transcendental realization there are three divisions of knowledge called prasthāna-traya. That department of knowledge which is proved by Vedic instruction (like the Upaniṣads) is called śruti-prasthāna. Authoritative books indicating the ultimate goal and written by liberated souls like Vyāsadeva (for example, Bhagavad-gītā, Mahābhārata and the Purāṇas, especially Śrīmad-Bhāgavatam, the Mahā-Purāṇa) are called smṛti-prasthāna. From Vedic literatures we understand that the Vedas originated from the breathing of Nārāyaṇa. Vyāsadeva, who is an incarnation of the power of Nārāyaṇa, has compiled the Vedānta-sūtra (nyāya-prasthāna), but according to Śaṅkara's commentaries, Apāntaratamā Ṛṣi is also accredited with having compiled the codes of Vedānta-sūtra. According to Lord Caitanya, the codes of the Pañcarātra and the codes of Vedānta are one and the same. Since the Vedānta-sūtra is compiled by Vyāsadeva, it should be understood to be spoken by Nārāyaṇa Himself. From all descriptive literatures dealing with Vedānta-sūtra, it appears that there were many other ṛṣis contemporary with Vyāsadeva who also discussed Vedānta-sūtra. These sages were Ātreya, Āśmarathya, Auḍulomi, Kārṣṇājini, Kāśakṛtsna, Jaimini, Bādarī and other sages such as Pārāśarī and Karmandī.
Actually in the first two chapters of Vedānta-sūtra the relationship between the living entities and the Supreme Lord is explained, and in the Third Chapter the discharge of devotional service is explained. The Fourth Chapter deals with the relationship which results from discharging devotional service. The natural commentary on Vedānta-sūtra is Śrīmad-Bhāgavatam. The great ācāryas of the four Vaiṣṇava communities (sampradāyas)—namely, Rāmānujācārya, Madhvācārya, Viṣṇu Svāmī and Nimbārka—have also written commentaries on Vedānta-sūtra by following the principles of Śrīmad-Bhāgavatam. At present the followers of all the ācāryas have written many books following the principles of Śrīmad-Bhāgavatam as the commentary on the Vedānta. Śaṅkara's commentary on Vedānta-sūtra, known as Śārīraka-bhāṣya, is very much adored by the impersonalist scholars, but commentaries written on the Vedānta written from the materialistic point of view are completely adverse to the transcendental service of the Lord. Consequently Lord Caitanya said that direct commentaries on the Upaniṣads and Vedānta-sūtra are glorious, but that anyone who follows the indirect path of Śaṅkarācārya's Śārīraka-bhāṣya is certainly doomed.