The LaTeX integration is one place where gnuplot really shines, and is one of the main reasons I use it. Aside from the epslatex (or cairolatex) workflow, gnuplot works with tikz: you can generate tikz drawing commands with gnuplot, or call out to gnuplot from tikz/PGFplots. So, to answer your question, I don't know of a better tool for what you want to do. You can also pipe the data and plotting commands to gnuplot from any programming language that supports a socket interface.

If you can forgive a plug, my new book about gnuplot is underway: https://alogus.com/publishing/gnuplot5/