Getting "better" fit indices for the same model in one program than another should make you suspicious. Did you really fit the same model? If so, the model should result in the same (or very close) fit indices across different programs. Only very minor differences would be expected. For example, some programs use N, others N - 1 in the formula for the chi-square test of model fit, which only makes a very small difference in most samples of reasonable size.
Aside from that, AMOS is perhaps somewhat more user-friendly than LISREL.
If you want to develop a new theory (exploratory research), then Smart PLS may be given preference and if you want to test a theory (confirmatory research), then AMOS seems a bit better than SmartPLS.
Most of my research has been exploratory and I have found SmartPLS to be better overall & the analysis reports to be more comprehensive.
Let me share a table to help you decide. Hope it helps :)