I have been using GATK IndelRealigner in non-GATK pipelines, and was wondering if there was a replacement option in the current GATK version, or if I should keep using the old version of GATK for indel realignment.
For now, you will have to continue to use GATK3 for indel realignment. There are ongoing efforts to make these tools available in GATK4 here and here. I cannot say when these efforts will be finalized.
Alternatively, remember that HaplotypeCaller performs reassembly and you can produce an activity profile, much like RelignerTargetCreator's active regions, with HaplotypeCaller's --assembly-region-out. Also, you can produce HaplotypeCaller reassembled reads using the -bamout option.
P.S. Perhaps LeftAlignIndels would be of interest to you another alternative.