Swami Vivekananda argues that the Ishvara of the Yoga school is not the same as the God of the Vedas and thus agrees with the Brahma Sutra criticism.
क्लेशकर्मविपाकाशयैरपरामृष्टः पुरुषविशेष ईश्वरः ॥२४॥
- Ishvara (the Supreme Ruler) is a special Purusha, untouched by misery, actions, their results, and desires.
We must again remember that the Pâtanjala Yoga philosophy is based
upon the Sankhya philosophy; only in the latter there is no place for
God, while with the Yogis God has a place. The Yogis, however, do not
mention many ideas about God, such as creating. God as the Creator of
the universe is not meant by the Ishvara of the Yogis. According to
the Vedas, Ishvara is the Creator of the universe; because it is
harmonious, it must be the manifestation of one will. The Yogis want
to establish a God, but they arrive at Him in a peculiar fashion of
their own. They say:
तत्र निरतिशयं सर्वज्ञत्वबीजम् ॥२५॥
- In Him becomes infinite that all-knowingness which in others is (only) a germ.
The mind must always travel between two extremes. You can think of
limited space, but that very idea gives you also unlimited space.
Close your eyes and think of a little space; at the same time that you
perceive the little circle, you have a circle round it of unlimited
dimensions. It is the same with time. Try to think of a second; you
will have, with the same act of perception, to think of time which is
unlimited. So with knowledge. Knowledge is only a germ in man, but you
will have to think of infinite knowledge around it, so that the very
constitution of our mind shows us that there is unlimited knowledge,
and the Yogis call that unlimited knowledge God.
The complete works of Swami Vivekananda, volume 1, Raja Yoga, Patanjali's Yoga aphorisms, I.24-25
However, Swami Vivekananda thought that such differences do not matter much. He does not refute the Yoga school.
Whether you are an Advaitin, whether you are a qualified monist or
dualist, it does not matter much. But let me draw your attention to
one thing which unfortunately we always forget: that is - "O man, have
faith in yourself." That is the way by which we have faith in God.
Whether you are an Advaitist or a dualist, whether you are a believer
in the system of Yoga or a believer in Shankaracharya, whether you are
a follower of Vyasa or Vishvamitra, it does not matter much.
The Complete Works of Swami Vivekananda, Volume 3, Lectures from Colombo to Almora, The influence of Indian spiritual thought in England