The Science of Science (SciSci) examines how scientific knowledge is generated, evaluated, and transformed by utilizing large-scale scholarly and bibliometric data. As these data grow in scale and complexity, analysis has increasingly relied on statistical, network-based, machine learning methods, and is now seeing growing involvement of AI agents. This emerging class of such agents, ranging from multi-agent simulations of scientific behavior to tool-augmented systems for empirical analysis, is beginning to reshape how SciSci research is conducted. In this survey, we propose a task-centered taxonomy, distinguishing *agents as simulations*, which model citation, collaboration, and community dynamics, from *agents as tools*, which assist empirical analysis and scientific workflows. We review agent architectures, learning mechanisms, evaluation, and SciSci benchmarks, and examine open challenges related to reliability, data quality, and bias. Our survey aims to clarify the landscape of AI agents in SciSci and to support the development of reliable and scientifically useful AI systems for studying science and scientific communities.