Villanueva is not a basque surname, is clearly a spanish one, the meaning of Villanueva is VILLA: Town, and NUEVA: NEW, is composed by two spanish words, Basque language is totally different from spanish VILLA or TOWN is URI or IRI, and NUEVA or NEW is BARRI or BERRI, as you can see, in many aspects spanish is more simmilar to english (Villa-Village, Nuevo-New) than to basque language.

In Spain there are many places with the name Villanueva, but most of them has a composed name Example: Villanueva de Arakil, or Villanueva del Rio or.....

In any case there has been since old times, families with this surname in the Basque Country.

One of the Greater authors about basque surname is Jaime Kerexeta, and he says in his book "Diccionario Onomastico y Heraldico vasco" VILLANUEVA: Is a linage originated in Aragon (Spain), there has been branches in the Basque Country (Spanish and French Basque Country) in Uhartehiri (Basse-Navarre-France), Gipuzkoa, Gordexola (Bizkaia), and Araba. In Onate (Gipuzkoa Province, Basque Country) lived a man surnamed Villanueva in 1388.

So, although the origin of the surname is not basque (since a linguistical point of view), there has been Villanueva families in the Basque Country (in all the basque provinces since long time ago), this make possible that the Villanueva you are speaking about, was a basque, there was a lot of Basque people in Philippines, I know a basque familie that had plantations in Negros, their surname is GAMBOA, and a woman of this familie is married with a man surnamed Villanueva (I don't think he has any relation with Philippines).

If you are interested I can transcribe the coat of arms of the Basque Villanuevas.