In short, no, certainly not in the late 1990s. He does not even figure in this organizational structure (below) of 1998, I compiled in 2011 based on info from former combatants.
For sure things had changed by 2003 and 2004 when the International Criminal Court (ICC) investigators dispatched to Northern Uganda to investigate (and when Ongwen allegedly carried out some of the crimes for which he is indicted.) But even then, Ongwen was not in the same leadership bracket as the other four indicted by the ICC. Joseph Kony, Vincent Otti, Okot Odhiambo and Raska Lukwiya were indeed top commanders in 2003-4 during the ICC investigations. They were also far more influential than Ongwen in 2005 when the indictments were unsealed and they remained more senior to Ongwen until their deaths (save Kony who is still alive).
Ongwen was not considered part of the top leadership of the LRA, not by Kony nor by other senior commanders, the people who were never abducted but joined the LRA in its early days. This becomes clear from conversations with former commanders who have defected recently and was also seen during the Juba Talks of 2006-2008. Throughout the talks, Ongwen was not seated with the top leadership which consisted of Kony, Otti, Odhiambo, Caesar Achellam, Bok Abudema, and Nixman Opuk Oryang (Achellam defected in 2012). (see for instance this picture from 2006 featuring Otti, Kony, Odhiambo and Abudema.)
In 2003 and 2004 when the ICC opened investigations on LRA crimes in Northern Uganda, there were other commanders more senior than Ongwen, who were not indicted. Many in Northern Uganda are still questioning how was it that Kenneth Banya, a senior advisor to Kony, captured by the Ugandan army in July 2004 was never prosecuted by the Ugandans or the ICC alike? Sam Kolo was well-known to the outside world as the LRA Political Commissar (he defected in 2005). Other prominent commanders included Abudema (killed in 2009), Opuk (likely killed after 2010), Tulu (or Tulu Box) and Onen Kamdulu (killed and defected in 2005, respectively), Ochan Bunia (likely died after 2010), Alphonse Lamola (alive in the bush) and many others.
Why is it then that the ICC prosecutor decided to indict Ongwen, abducted as a child, alongside the likes of Kony, Otti, Odhiambo and Lukwiya, all commanders who joined voluntarily and engineered the abductions of thousands of people, including Ongwen? Why did the prosecutor decide to leave out more senior commanders than Ongwen, even some like Achellam or Abudema who were not abducted but joined from the early LRA days? Were Ongwen’s crimes perceived as more heinous than those perpetrated by other fighters? Here’s hoping that the on-going case will answer these and many more questions.