Yes, you can use the GenomicInteractions package with 4C-seq data! It is designed to be suitable for any 3D genome interaction method. The makeGenomicInteractionsFromFile function gives some options for importing data, depending on the format of your input file. If your input is not in a format that is supported for direct import, then as a general rule, you will want to provide the constructor function with three things: (1) a GRanges of "anchors" for interactions, in this case your viewpoint region, (2) another GRanges of anchors for interactions, in this case your interacting regions, and (3) a vector of interaction strengths for each pair of GRanges.
Hope that helps and thanks for your interest in the package!